Merge pull request #4187 from IQSS/develop

v4.8.1

doc/sphinx-guides/source/conf.py

@@ -64,9 +64,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '4.8'
+version = '4.8.1'
 # The full version, including alpha/beta/rc tags.
-release = '4.8'
+release = '4.8.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/sphinx-guides/source/index.rst

@@ -3,7 +3,7 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Dataverse 4.8 Guides
+Dataverse 4.8.1 Guides
 ======================
 
 These guides are for the most recent version of Dataverse. For the guides for **version 4.7.1** please go `here <http://guides.dataverse.org/en/4.7.1/>`_.

pom.xml

@@ -4,7 +4,7 @@
 
     <groupId>edu.harvard.iq</groupId>
     <artifactId>dataverse</artifactId>
-    <version>4.8</version>
+    <version>4.8.1</version>
     <packaging>war</packaging>
 
     <name>dataverse</name>

src/main/java/Bundle.properties

@@ -550,7 +550,7 @@ notification.email.verifyEmail.subject={0}: Verify your email address
 notification.email.greeting=Hello, \n
 # Bundle file editors, please note that "notification.email.welcome" is used in a unit test
 notification.email.welcome=Welcome to {0}! Get started by adding or finding data. Have questions? Check out the User Guide at {1}/{2}/user or contact {3} at {4} for assistance.
-notification.email.welcomeConfirmEmailAddOn=\n\nPlease verify your email address at {0}. Note, the verify link will expire after {1}. Send another verification email by visiting your account page.
+notification.email.welcomeConfirmEmailAddOn=\n\nPlease verify your email address at {0} . Note, the verify link will expire after {1}. Send another verification email by visiting your account page.
 notification.email.requestFileAccess=File access requested for dataset: {0}. Manage permissions at {1}.
 notification.email.grantFileAccess=Access granted for files in dataset: {0} (view at {1}).
 notification.email.rejectFileAccess=Your request for access was rejected for the requested files in the dataset: {0} (view at {1}). If you have any questions about why your request was rejected, you may reach the dataset owner using the "Contact" link on the upper right corner of the dataset page.

src/main/java/edu/harvard/iq/dataverse/DataFile.java

@@ -949,15 +949,6 @@ public String getCreateDateFormattedYYYYMMDD() {
         return null;
     }
 
-
-    public String getThumbnailString() {
-        DatasetThumbnail datasetThumbnail = FileUtil.getThumbnail(this);
-        if (datasetThumbnail == null) {
-            return null;
-        }
-        return datasetThumbnail.getBase64image();
-    }
-
 
 } // end of class
 

src/main/java/edu/harvard/iq/dataverse/DatasetPage.java

@@ -49,8 +49,6 @@
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.nio.file.Files;
-import java.nio.file.Paths;
 import java.sql.Timestamp;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
@@ -82,10 +80,7 @@
 import edu.harvard.iq.dataverse.datasetutility.TwoRavensHelper;
 import edu.harvard.iq.dataverse.datasetutility.WorldMapPermissionHelper;
 import edu.harvard.iq.dataverse.engine.command.impl.RequestRsyncScriptCommand;
-import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
-import edu.harvard.iq.dataverse.engine.command.impl.AddLockCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.PublishDatasetResult;
-import edu.harvard.iq.dataverse.engine.command.impl.RemoveLockCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.RestrictFileCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.ReturnDatasetToAuthorCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.SubmitDatasetForReviewCommand;
@@ -286,7 +281,7 @@ public String getRsyncScriptFilename() {
     public String getThumbnailString() {
         // This method gets called 30 (!) times, just to load the page!
         // - so let's cache that string the first time it's called. 
-
+            
         if (thumbnailString != null) {
             if ("".equals(thumbnailString)) {
                 return null;
@@ -439,19 +434,9 @@ public void setDataverseSiteUrl(String dataverseSiteUrl) {
         this.dataverseSiteUrl = dataverseSiteUrl;
     }
 
-    public List<FileMetadata> getDatasetFileMetadatas() {
-        Long datasetVersion = workingVersion.getId();
-        if (datasetVersion != null) {
-                int unlimited = 0;
-                int maxResults = unlimited;
-            return datafileService.findFileMetadataByDatasetVersionId(datasetVersion, maxResults, fileSortField, fileSortOrder);     
-        } 
-        return null; 
-    }
-
     public DataFile getInitialDataFile() {
-        if (getDatasetFileMetadatas() != null && getDatasetFileMetadatas().size() > 0) {
-            return getDatasetFileMetadatas().get(0).getDataFile();
+        if (workingVersion.getFileMetadatas() != null && workingVersion.getFileMetadatas().size() > 0) {
+            return workingVersion.getFileMetadatas().get(0).getDataFile();
         }
         return null;
     }
@@ -488,10 +473,10 @@ public void setSwiftContainerName(String name){
 
     }
     //This function applies to an entire dataset
-    public boolean isSwiftStorage() {
+    private boolean isSwiftStorage() {
         //containers without datafiles will not be stored in swift storage
         if (getInitialDataFile() != null){
-            for (FileMetadata fmd : getDatasetFileMetadatas()) {
+            for (FileMetadata fmd : workingVersion.getFileMetadatas()) {
                 //if any of the datafiles are stored in swift
                 if (fmd.getDataFile().getStorageIdentifier().startsWith("swift://")) {
                     return true;
@@ -502,31 +487,51 @@ public boolean isSwiftStorage() {
     }
 
     //This function applies to a single datafile
-    public boolean isSwiftStorage(FileMetadata metadata){
+    private boolean isSwiftStorage(FileMetadata metadata){
         if (metadata.getDataFile().getStorageIdentifier().startsWith("swift://")) {
             return true;
         }
         return false;
     }
 
+
+    private Boolean showComputeButtonForDataset = null;
     //This function applies to an entire dataset
     public boolean showComputeButton() {
+        if (showComputeButtonForDataset != null) {
+            return showComputeButtonForDataset;
+        }
+
         if (isSwiftStorage() && (settingsService.getValueForKey(SettingsServiceBean.Key.ComputeBaseUrl) != null)) {
-            return true;
+            showComputeButtonForDataset = true;
+        } else {
+            showComputeButtonForDataset = false;
         }
-        return false;
+        return showComputeButtonForDataset;
     }
 
+    private Map<Long, Boolean> showComputeButtonForFile = new HashMap<>();
     //this function applies to a single datafile
     public boolean showComputeButton(FileMetadata metadata) {
-        if (isSwiftStorage(metadata) && (settingsService.getValueForKey(SettingsServiceBean.Key.ComputeBaseUrl) != null)) {
-            return true;
+        Long fileId = metadata.getDataFile().getId();
+
+        if (fileId == null) {
+            return false;
         }
-        return false;
+
+        if (showComputeButtonForFile.containsKey(fileId)) {
+            return showComputeButtonForFile.get(fileId);
+        }
+
+        boolean result = isSwiftStorage(metadata) 
+                && settingsService.getValueForKey(SettingsServiceBean.Key.ComputeBaseUrl) != null;
+
+        showComputeButtonForFile.put(fileId, result);
+        return result;
     }
 
     public boolean canDownloadAllFiles(){
-       for (FileMetadata fmd : getDatasetFileMetadatas()) {
+       for (FileMetadata fmd : workingVersion.getFileMetadatas()) {
             if (!fileDownloadHelper.canDownloadFile(fmd)) {
                 return false;
             }
@@ -548,8 +553,8 @@ public String getComputeUrl() throws IOException {
         SwiftAccessIO swiftObject = getSwiftObject();
         if (swiftObject != null) {
             swiftObject.open();
-            if (settingsService.isTrueForKey(SettingsServiceBean.Key.PublicInstall, false)) {
-                return settingsService.getValueForKey(SettingsServiceBean.Key.ComputeBaseUrl) + "?containerName=" + swiftObject.getSwiftContainerName();
+            if (settingsWrapper.isTrueForKey(SettingsServiceBean.Key.PublicInstall, false)) {
+                return settingsWrapper.getValueForKey(SettingsServiceBean.Key.ComputeBaseUrl) + "?containerName=" + swiftObject.getSwiftContainerName();
             }
             //assuming we are able to get a temp url for a dataset
             return settingsWrapper.getValueForKey(SettingsServiceBean.Key.ComputeBaseUrl) + "?containerName=" + swiftObject.getSwiftContainerName() + "&temp_url_sig=" + swiftObject.getTempUrlSignature() + "&temp_url_expires=" + swiftObject.getTempUrlExpiry();
@@ -571,8 +576,8 @@ public String getComputeUrl(FileMetadata metadata) {
         } catch (IOException e) {
             logger.info("DatasetPage: Failed to get storageIO");
         }
-        if (settingsService.isTrueForKey(SettingsServiceBean.Key.PublicInstall, false)) {
-            return settingsService.getValueForKey(SettingsServiceBean.Key.ComputeBaseUrl) + "?containerName=" + swiftObject.getSwiftContainerName() + "&objectName=" + swiftObject.getSwiftFileName();
+        if (settingsWrapper.isTrueForKey(SettingsServiceBean.Key.PublicInstall, false)) {
+            return settingsWrapper.getValueForKey(SettingsServiceBean.Key.ComputeBaseUrl) + "?containerName=" + swiftObject.getSwiftContainerName() + "&objectName=" + swiftObject.getSwiftFileName();
         }
 
         return settingsWrapper.getValueForKey(SettingsServiceBean.Key.ComputeBaseUrl) + "?containerName=" + swiftObject.getSwiftContainerName() + "&objectName=" + swiftObject.getSwiftFileName() + "&temp_url_sig=" + swiftObject.getTempUrlSignature() + "&temp_url_expires=" + swiftObject.getTempUrlExpiry();
@@ -700,9 +705,8 @@ public boolean isThumbnailAvailable(FileMetadata fileMetadata) {
 
         // new and optimized logic: 
         // - check download permission here (should be cached - so it's free!)
-        // - only then ask the file service if the thumbnail is available/exists.
-        // the service itself no longer checks download permissions.  
-        // plus, cache the results!
+        // - only then check if the thumbnail is available/exists.
+        // then cache the results!
 
         Long dataFileId = fileMetadata.getDataFile().getId();
 
@@ -1416,7 +1420,7 @@ private String init(boolean initFull) {
                 this.loadMapLayerMetadataLookup();  // A DataFile may have a related MapLayerMetadata object
                 this.guestbookResponse = guestbookResponseService.initGuestbookResponseForFragment(dataset, null, session);
                 logger.fine("Checking if rsync support is enabled.");
-                if (DataCaptureModuleUtil.rsyncSupportEnabled(settingsService.getValueForKey(SettingsServiceBean.Key.UploadMethods))) {
+                if (DataCaptureModuleUtil.rsyncSupportEnabled(settingsWrapper.getValueForKey(SettingsServiceBean.Key.UploadMethods))) {
                     try {
                         ScriptRequestResponse scriptRequestResponse = commandEngine.submit(new RequestRsyncScriptCommand(dvRequestService.getDataverseRequest(), dataset));
                         logger.fine("script: " + scriptRequestResponse.getScript());
@@ -1472,7 +1476,7 @@ private String init(boolean initFull) {
                 updateDatasetFieldInputLevels();
             }
 
-            if (settingsService.isTrueForKey(SettingsServiceBean.Key.PublicInstall, false)){
+            if (settingsWrapper.isTrueForKey(SettingsServiceBean.Key.PublicInstall, false)){
                 JH.addMessage(FacesMessage.SEVERITY_WARN, BundleUtil.getStringFromBundle("dataset.message.publicInstall"));
             }
 
@@ -1482,7 +1486,7 @@ private String init(boolean initFull) {
         } else {
             return permissionsWrapper.notFound();
         }
-       try {
+        try {
             privateUrl = commandEngine.submit(new GetPrivateUrlCommand(dvRequestService.getDataverseRequest(), dataset));
             if (privateUrl != null) {
                 JH.addMessage(FacesMessage.SEVERITY_INFO, BundleUtil.getStringFromBundle("dataset.privateurl.infoMessageAuthor", Arrays.asList(getPrivateUrlLink(privateUrl))));
@@ -3516,13 +3520,21 @@ public void saveAdvancedOptions() {
         fileMetadataSelectedForIngestOptionsPopup = null;
     }
 
+    private Boolean downloadButtonAvailable = null; 
 
     public boolean isDownloadButtonAvailable(){
+
+        if (downloadButtonAvailable != null) {
+            return downloadButtonAvailable;
+        }
+
         for (FileMetadata fmd : workingVersion.getFileMetadatas()) {
             if (this.fileDownloadHelper.canDownloadFile(fmd)) {
+                downloadButtonAvailable = true;
                 return true;
             }
         }
+        downloadButtonAvailable = false;
         return false;
     }
 
@@ -3968,7 +3980,7 @@ public String finishRsyncScriptAction() {
      * 
      */
     public List<DatasetField> getDatasetSummaryFields() {
-       customFields  = settingsService.getValueForKey(SettingsServiceBean.Key.CustomDatasetSummaryFields);
+       customFields  = settingsWrapper.getValueForKey(SettingsServiceBean.Key.CustomDatasetSummaryFields);
 
         return DatasetUtil.getDatasetSummaryFields(workingVersion, customFields);
     }

src/main/java/edu/harvard/iq/dataverse/api/HarvestingServer.java

@@ -55,7 +55,7 @@ public class HarvestingServer extends AbstractApiBean {
     // TODO: this should be available to admin only.
 
     @GET
-    @Path("")
+    @Path("/")
     public Response oaiSets(@QueryParam("key") String apiKey) throws IOException {